# ========= [INFO] ==========
# Mut inCB: not accepter mutation in BC
# Mut inMS: 2
# ReadIn  : /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.unmapped.bam
# seq_deb : CATGTAGTC
# seq_fin : TCTCT
# MS_seq : A
# excl : C,G,T
# nom  : A15
# =============================
#
#-------------- Filt ------------------
# condiGrep: CATG.AGTC[ATCGN]+AAAAA[ATCGN]+.CTCT|CATG.AGTC[ATCGN]+AAAAA[ATCGN]+T.TCT|CATG.AGTC[ATCGN]+AAAAA[ATCGN]+TC.CT|CATG.AGTC[ATCGN]+AAAAA[ATCGN]+TCT.T|CATG.AGTC[ATCGN]+AAAAA[ATCGN]+TCTC.|CATGT.GTC[ATCGN]+AAAAA[ATCGN]+.CTCT|CATGT.GTC[ATCGN]+AAAAA[ATCGN]+T.TCT|CATGT.GTC[ATCGN]+AAAAA[ATCGN]+TC.CT|CATGT.GTC[ATCGN]+AAAAA[ATCGN]+TCT.T|CATGT.GTC[ATCGN]+AAAAA[ATCGN]+TCTC.|CATGTA.TC[ATCGN]+AAAAA[ATCGN]+.CTCT|CATGTA.TC[ATCGN]+AAAAA[ATCGN]+T.TCT|CATGTA.TC[ATCGN]+AAAAA[ATCGN]+TC.CT|CATGTA.TC[ATCGN]+AAAAA[ATCGN]+TCT.T|CATGTA.TC[ATCGN]+AAAAA[ATCGN]+TCTC.|CATGTAG.C[ATCGN]+AAAAA[ATCGN]+.CTCT|CATGTAG.C[ATCGN]+AAAAA[ATCGN]+T.TCT|CATGTAG.C[ATCGN]+AAAAA[ATCGN]+TC.CT|CATGTAG.C[ATCGN]+AAAAA[ATCGN]+TCT.T|CATGTAG.C[ATCGN]+AAAAA[ATCGN]+TCTC.|CATGTAGT.[ATCGN]+AAAAA[ATCGN]+.CTCT|CATGTAGT.[ATCGN]+AAAAA[ATCGN]+T.TCT|CATGTAGT.[ATCGN]+AAAAA[ATCGN]+TC.CT|CATGTAGT.[ATCGN]+AAAAA[ATCGN]+TCT.T|CATGTAGT.[ATCGN]+AAAAA[ATCGN]+TCTC.
# condiGrep Rev-Compt: .GAGA[NCGAT]+TTTTT[NCGAT]+.ACTACATG|A.AGA[NCGAT]+TTTTT[NCGAT]+.ACTACATG|AG.GA[NCGAT]+TTTTT[NCGAT]+.ACTACATG|AGA.A[NCGAT]+TTTTT[NCGAT]+.ACTACATG|AGAG.[NCGAT]+TTTTT[NCGAT]+.ACTACATG|.GAGA[NCGAT]+TTTTT[NCGAT]+G.CTACATG|A.AGA[NCGAT]+TTTTT[NCGAT]+G.CTACATG|AG.GA[NCGAT]+TTTTT[NCGAT]+G.CTACATG|AGA.A[NCGAT]+TTTTT[NCGAT]+G.CTACATG|AGAG.[NCGAT]+TTTTT[NCGAT]+G.CTACATG|.GAGA[NCGAT]+TTTTT[NCGAT]+GA.TACATG|A.AGA[NCGAT]+TTTTT[NCGAT]+GA.TACATG|AG.GA[NCGAT]+TTTTT[NCGAT]+GA.TACATG|AGA.A[NCGAT]+TTTTT[NCGAT]+GA.TACATG|AGAG.[NCGAT]+TTTTT[NCGAT]+GA.TACATG|.GAGA[NCGAT]+TTTTT[NCGAT]+GAC.ACATG|A.AGA[NCGAT]+TTTTT[NCGAT]+GAC.ACATG|AG.GA[NCGAT]+TTTTT[NCGAT]+GAC.ACATG|AGA.A[NCGAT]+TTTTT[NCGAT]+GAC.ACATG|AGAG.[NCGAT]+TTTTT[NCGAT]+GAC.ACATG|.GAGA[NCGAT]+TTTTT[NCGAT]+GACT.CATG|A.AGA[NCGAT]+TTTTT[NCGAT]+GACT.CATG|AG.GA[NCGAT]+TTTTT[NCGAT]+GACT.CATG|AGA.A[NCGAT]+TTTTT[NCGAT]+GACT.CATG|AGAG.[NCGAT]+TTTTT[NCGAT]+GACT.CATG
#--------------------------------------
module load picard/2.8.2
> java -jar /env/gfs/apps/picard/2.8.2/picard.jar SortSam I=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.unmapped.sam O=/env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.unmapped.sort.sam SORT_ORDER=queryname 
# [Creat: /env/gfs/Projects/yshen/21_SophieMS_Iseq100/Papier/Example/Example_II.1/Output/3_BAM_Fusion_min3ReadByGrp/7-N3-12cycles-IDT.A15.unmapped.bam ]
